The process of plant domestication is often protracted, involving under-explored intermediate stages with important implications for the evolutionary trajectories of domestication traits. Previously, tomato domestication history has been thought to involve two major transitions: one from wild Solanum pimpinellifolium L. (SP) to a semi-domesticated intermediate, S. lycoperiscum L. var. cerasiforme (SLC) in South America, and a second transition from SLC to fully domesticated S. lycopersicum L. var. lycopersicum (SLL) in Mesoamerica. In this study, we employ population genomic methods to reconstruct tomato domestication history, focusing on the evolutionary changes occurring in the intermediate stages. Our results suggest that the origin of SLC may predate domestication, and that many traits considered typical of cultivated tomatoes arose in South American SLC, but were lost or diminished once these partially domesticated forms spread northward. These traits were then likely reselected in a convergent fashion in the common cultivated tomato, prior to its expansion around the world. Based on these findings, we reveal complexities in the intermediate stage of tomato domestication and provide insight on trajectories of genes and phenotypes involved in tomato domestication syndrome. Our results also allow us to identify underexplored germplasm that harbors useful alleles for crop improvement.

中文翻译：

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拉丁美洲栽培番茄复杂驯化史的基因组证据。

植物驯化的过程通常是漫长的，涉及开发不足的中间阶段，对驯化性状的进化轨迹具有重要意义。以前，番茄的驯化历史被认为涉及两个主要转变：一个是从野生茄形变色龙（SP）到半驯化的中间变种S. lycoperiscum L. var。南美地区的蓝藻（SLC），以及从SLC到完全驯化的S. lycopersicum L. var的第二次过渡。中美洲的lycopersicum（SLL）。在这项研究中，我们采用种群基因组学方法来重建番茄驯化的历史，重点是中间阶段发生的进化变化。我们的结果表明，SLC的起源可能早于驯化，南美SLC出现了许多被认为是典型栽培番茄的特征，但是一旦这些部分驯化的形式向北传播，这些特征便会消失或消失。然后，在将其扩展至世界各地之前，可以在普通栽培番茄中以融合的方式重新选择这些特性。基于这些发现，我们揭示了番茄驯化中间阶段的复杂性，并提供了与番茄驯化综合症有关的基因和表型轨迹的见解。我们的结果还使我们能够鉴定出未开发的种质，这些种质具有用于作物改良的有用等位基因。在扩展到全球之前。基于这些发现，我们揭示了番茄驯化中间阶段的复杂性，并提供了与番茄驯化综合症有关的基因和表型轨迹的见解。我们的结果还使我们能够鉴定出未开发的种质，这些种质具有用于作物改良的有用等位基因。在扩展到全球之前。基于这些发现，我们揭示了番茄驯化中间阶段的复杂性，并提供了与番茄驯化综合症有关的基因和表型轨迹的见解。我们的结果还使我们能够鉴定出未开发的种质，这些种质具有用于作物改良的有用等位基因。